import warnings
import sys
import os
import numpy as np
import pandas as pd
import scanpy as sc
import loompy as lp
import pyscenic
warnings.filterwarnings('ignore')

Human Myocardial Infaction Dataset

The dataset in from the paper Spatial multi-omic map of human myocardial infarction Kuppe, C. et.al., 2022. The following gives an overview of the dataset

Human_MI = sc.read_h5ad('/rwthfs/rz/cluster/home/noco0013/projects/mi_hearts/snRNA/snRNA-seq-submission_subcluster.h5ad')

sc.set_figure_params(frameon=False, dpi=200, fontsize=8)
sc.pl.umap(Human_MI, color=['cell_type_original', 'major_labl','annotation'], 
           title=['Major Cell type','Disease Condition', 'Cell Subtypes'], ncols=3)

KPMP Kidney Tissue Dataset

The Kidney Precision Medicine Project based Kidney Tissue Information is taken into consideration for analysis

kpmp = sc.read_h5ad("/rwthfs/rz/cluster/work/sw362433/KPMP/kpmp.h5ad")

sc.set_figure_params(frameon=False, dpi=150, fontsize=8)
sc.pl.umap(kpmp, color=['myconditions', 'subclass.l1','mysubtypes'], 
           title=['Disease Condition', 'Cell types',
                 'Subtypes'], ncols=3)